# List of top-scoring protein chains for t04-100-30-alpha-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.soe.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 3h3mA 126 4.65e-13 2jg0A 535 2.42e-02 a.102.1.9 148034 2avkA 136 2.78e-01 2jx0A 135 5.84e-01 2qk2A 242 7.29e-01 3eb2A 300 7.98e-01 2cy8A 453 8.47e-01 2i76A 276 9.14e-01 a.100.1.10,c.2.1.6 147535,147536 1nu7D 282 1.01e+00 a.8.6.1,a.8.6.1 92191,92192 2a1dD 329 1.53e+00 2uubT 106 1.61e+00 a.7.6.1 139951 3bc1B 59 1.69e+00 1fjgT 106 1.90e+00 1fjfT a.7.6.1 16338 1n8vA 112 3.65e+00 a.118.21.1 85457 1bs0A 384 3.66e+00 1bs0A c.67.1.4 34490 3stdA 165 3.87e+00 3stdA d.17.4.1 38073 2of3A 266 3.96e+00 1std 172 4.00e+00 3stdA 2f6hX 419 4.10e+00 1ufaA 520 4.15e+00 a.8.3.3,c.6.2.4 99329,99330 4blmA 265 4.21e+00 1btl e.3.1.1 42721 3hjeA 704 4.34e+00 1ppjA 446 4.49e+00 d.185.1.1,d.185.1.1 104252,104253 2ccyA 128 4.76e+00 2ccyA a.24.3.2 16544 2fztA 79 4.76e+00 a.46.3.1 134476 2vqeT 106 4.78e+00 a.7.6.1 153444 2gscA 128 4.82e+00 a.29.16.1 147169 2ux0A 143 4.92e+00 d.17.4.7 152231 1ek9A 428 5.05e+00 1ek9A f.5.1.1 43809 1idpA 172 5.25e+00 d.17.4.1 83685 2vj4A 294 5.52e+00 1tzvA 142 5.57e+00 a.79.1.1 107526 2be3A 226 5.76e+00 d.218.1.8 128349 1woyA 500 5.84e+00 a.27.1.1,c.26.1.1 121130,121131 1ux8A 132 5.84e+00 a.1.1.1 113449 2oy9A 98 5.95e+00 a.276.1.1 149063 2novA 496 6.01e+00 1e85A 127 6.37e+00 1bbhA a.24.3.2 16549 3lbxB 185 6.61e+00 2pqxA 245 6.83e+00 2qcxA 263 7.00e+00 3bomA 142 7.26e+00 1ng6A 148 7.43e+00 a.182.1.1 85670 2v6xA 85 7.47e+00 1syyA 346 7.51e+00 a.25.1.2 106126 1z0kB 69 7.87e+00 a.2.19.1 124322 1pd3A 58 8.27e+00 a.30.3.1 94512 2yxhA 116 8.32e+00 2d5bA 500 8.32e+00 a.27.1.1,c.26.1.1 131268,131269 1qazA 351 8.55e+00 1qazA a.102.3.1 18848 1fcyA 236 8.81e+00 2lbd a.123.1.1 19282 1w33A 181 9.02e+00 3cjhB 64 9.35e+00 1nkpA 88 9.54e+00 a.38.1.1 80573 2dobA 83 9.69e+00 2gs8A 317 9.71e+00 2d7dB 40 1.02e+01 2rd3A 223 1.06e+01 1a8h 500 1.07e+01 1a8h 1dmgA 225 1.07e+01 1dmgA c.22.1.1 31036 1t7rA 269 1.08e+01 a.123.1.1 106635 1a5t 334 1.11e+01 1a5t 1a5tA 334 1.11e+01 a.80.1.1,c.37.1.20 18450,32423 1yzmA 51 1.14e+01 a.2.19.1 124283 2hkjA 469 1.16e+01 a.156.1.3,d.14.1.3,d.122.1.2 136553,136554,136555 1b5tA 275 1.16e+01 1b5tA c.1.23.1 29676 1w0bA 102 1.17e+01 a.7.11.1 108985 3fwkA 308 1.19e+01 2p06A 114 1.20e+01 a.204.1.3 139452 3ee4A 323 1.20e+01 2jabA 136 1.22e+01 3i0yA 140 1.22e+01 2vdeA 460 1.26e+01 1uedA 406 1.26e+01 a.104.1.1 99256 3cp5A 124 1.28e+01 3c5aA 264 1.28e+01 1eerA 166 1.29e+01 1eerA a.26.1.2 16846 1xg2B 153 1.36e+01 1ykjA 394 1.38e+01 c.3.1.2,d.16.1.2 145914,145915 1mu5A 471 1.39e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 2ie4A 589 1.40e+01 a.118.1.2 137291 1xkyA 301 1.40e+01 c.1.10.1 122094 2vqeM 126 1.41e+01 a.156.1.1 153437 1mx0A 472 1.43e+01 a.156.1.3,d.14.1.3,d.122.1.2 79618,79619,79620 2r9iA 141 1.45e+01 2z5kA 890 1.45e+01 1i2sA 282 1.45e+01 e.3.1.1 71104 3f2bA 1041 1.47e+01 3dghA 483 1.48e+01 1eyhA 144 1.51e+01 1eduA a.118.9.1 19214 2f2aC 100 1.52e+01 a.137.12.1 132804 2k37A 59 1.53e+01 2e2aA 105 1.54e+01 a.7.2.1 88499 2qsbA 89 1.55e+01 a.29.14.1 151315 3lxzA 229 1.56e+01 2cchB 260 1.58e+01 a.74.1.1,a.74.1.1 130237,130238 1tazA 365 1.59e+01 a.211.1.2 106734 2wk0A 265 1.62e+01 2fjbA 643 1.66e+01 2ov5A 261 1.71e+01 3hinA 275 1.71e+01 1yioA 208 1.71e+01 a.4.6.2,c.23.1.1 123326,123327 1vin 268 1.74e+01 1vin 1ihgA 370 1.75e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 2crbA 97 1.76e+01 a.7.16.1 130737 3lkeA 263 1.78e+01 1pbe 394 1.79e+01 1pbe 1pbeA 394 1.79e+01 c.3.1.2,d.16.1.2 30338,37869 2o5cA 659 1.81e+01 1r4gA 53 1.83e+01 a.8.5.1 96996 1fjgM 126 1.84e+01 1fjfM a.156.1.1 16293 2nl9A 157 1.85e+01 1gc5A 467 1.85e+01 1gc5A c.72.1.3 60429 2o7iA 592 1.87e+01 2q4xA 221 1.89e+01 a.132.1.3 139880 1b3uA 588 1.91e+01 1b3uA a.118.1.2 19135 1xcgA 368 1.91e+01 a.87.1.1,b.55.1.1 115120,115121 1qojA 63 1.92e+01 1qojA a.2.9.1 15716 1vctA 205 1.94e+01 a.7.12.1,d.286.1.1 119986,119987 2bkkA 264 1.95e+01 1wleA 501 1.96e+01 3dw0A 294 1.96e+01 1ez3A 127 1.97e+01 1dn1B a.47.2.1 17768 2cb0A 333 2.01e+01 2r9zA 463 2.01e+01 1jnrA 643 2.02e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1awcB 153 2.06e+01 1bd8 d.211.1.1 19156 3dr9A 137 2.06e+01 2hr2A 159 2.09e+01 a.118.8.8 147369 1jocA 125 2.10e+01 g.50.1.1,h.1.21.1 66990,66991 1k0iA 394 2.12e+01 c.3.1.2,d.16.1.2 67942,67943 2gkpA 167 2.16e+01 d.351.1.1 147129 1qkrA 188 2.18e+01 1qkrA a.24.9.1 16628 3kj0A 158 2.19e+01 1ihbA 162 2.20e+01 1bd8 d.211.1.1 19161 2x1nB 261 2.23e+01 3ltoA 323 2.23e+01 1e2aA 105 2.36e+01 1e2aA a.7.2.1 16322 2qfnA 138 2.36e+01 3h5dA 311 2.37e+01 1o9iA 266 2.38e+01 a.25.1.3 92671 1siqA 392 2.39e+01 a.29.3.1,e.6.1.1 105585,105586 1tyhA 248 2.39e+01 a.132.1.3 107458 3f5xB 256 2.40e+01 1moq 368 2.41e+01 1moq 1moqA 368 2.41e+01 c.80.1.1 35302 2c1nA 258 2.42e+01 a.118.7.1 129640 1f74A 293 2.44e+01 1nal3 c.1.10.1 29079 1itwA 741 2.47e+01 c.77.1.2 76793 1b0b 142 2.48e+01 2fal 1b0bA 142 2.48e+01 a.1.1.2 15010 1qjbA 245 2.49e+01 1qjaA a.118.7.1 19202 1gw5A 621 2.51e+01 a.118.1.10 70629 1gesA 450 2.52e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1yljA 263 2.56e+01 3kjdA 368 2.60e+01 2h88C 140 2.62e+01 3ixfA 137 2.62e+01 2e5fA 325 2.64e+01 1yakA 263 2.65e+01 a.132.1.3 122833 2w31A 162 2.66e+01 1hkxA 147 2.66e+01 d.17.4.7 83567 1vmbA 140 2.67e+01 d.58.14.1 113672 1ew6A 137 2.68e+01 1ewaA a.1.1.2 15637 1l8dA 112 2.69e+01 h.4.12.1 73687 2vglA 621 2.71e+01 1h6qA 168 2.73e+01 1h6qA b.88.1.2 60692 2p74A 263 2.76e+01 1vhcA 224 2.77e+01 c.1.10.1 100661 2cjeA 268 2.80e+01 1he1A 135 2.83e+01 1he1A a.24.11.1 16641 3ip4C 100 2.84e+01 1jkvA 266 2.85e+01 a.25.1.3 71719 1vh6A 145 2.87e+01 a.24.19.1 100644 1n97A 389 2.87e+01 a.104.1.1 80335 3kwsA 287 2.92e+01 2df8A 325 2.92e+01 1hzoA 271 3.00e+01 e.3.1.1 71092 1qwrA 319 3.00e+01 b.82.1.3 96491 2oieA 111 3.07e+01 a.204.1.2 139092 3figA 646 3.10e+01 3fvcA 663 3.11e+01 2fqmA 75 3.19e+01 d.378.1.1 147042 1wm5A 208 3.20e+01 a.118.8.1 121028 3cveA 72 3.23e+01 1or7A 194 3.23e+01 a.4.13.2,a.177.1.1 87332,87333 1zroA 602 3.25e+01 a.264.1.1,a.264.1.1 125551,125552 1qsaA 618 3.29e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 3epsA 578 3.31e+01 1hh8A 213 3.33e+01 1e96B a.118.8.1 61042 2ojpA 292 3.34e+01 3dc5A 195 3.34e+01 1jhgA 101 3.37e+01 1jhgA a.4.12.1 19009 2fbwC 141 3.39e+01 2qkwA 164 3.43e+01 a.8.8.1 150848 2p58B 86 3.45e+01 1y74A 57 3.48e+01 a.194.1.1 122679 3lxgA 308 3.52e+01 2b34A 199 3.60e+01 3hmhA 155 3.64e+01 2chpA 153 3.64e+01 1kx5B 102 3.68e+01 a.22.1.1 77594 1fc4A 401 3.70e+01 1bs0A c.67.1.4 59760 1dhpA 292 3.70e+01 1dhpA c.1.10.1 29097 1tmxA 293 3.70e+01 1rxxA 421 3.71e+01 d.126.1.4 98061 3kezA 461 3.75e+01 2w2dB 431 3.75e+01 3cqxC 88 3.77e+01 1miwA 404 3.82e+01 a.173.1.1,d.218.1.4 79162,79163 2bneA 241 3.82e+01 c.73.1.3 128824 3a01A 93 3.83e+01 1sqsA 242 3.84e+01 c.23.5.5 98968 1cpq 129 3.87e+01 1cpq 1cpqA 129 3.87e+01 a.24.3.2 16556 3lygA 120 3.89e+01 2qluA 314 3.91e+01 1iysA 262 3.92e+01 e.3.1.1 90723 3jw4A 148 3.94e+01 2rfgA 297 3.96e+01 3a1gB 40 3.97e+01 3dynA 329 3.98e+01 a.211.1.2 157942 2grrB 170 4.01e+01 a.118.12.1 147168 3fmsA 209 4.01e+01 2tpt 440 4.02e+01 1brwA 3hymB 330 4.06e+01 1tzyD 103 4.09e+01 a.22.1.1 107533 1dofA 403 4.11e+01 1c3cA a.127.1.1 19429 1otvA 259 4.15e+01 a.132.1.4 93526 1fe6C 52 4.20e+01 1fe6C h.1.19.1 45664 1wzuA 300 4.21e+01 c.145.1.1 121528 1it2A 146 4.24e+01 a.1.1.2 66365 3kq4A 393 4.25e+01 1nt2B 258 4.25e+01 a.183.1.1 86150 2ax6A 256 4.27e+01 a.123.1.1 127479 1h6gA 256 4.28e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 3fgaB 403 4.31e+01 3f1iH 98 4.33e+01 1sr9A 644 4.36e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1rkeA 262 4.37e+01 a.24.9.1,a.24.9.1 97608,97609 2hueC 84 4.38e+01 a.22.1.1 136776 2qzgA 94 4.38e+01 a.29.14.1 151482 1elwA 118 4.42e+01 1a17 a.118.8.1 19207 1fe6A 52 4.47e+01 1fe6A h.1.19.1 45662 2d4xA 248 4.50e+01 3gfvA 303 4.51e+01 3d3bA 141 4.53e+01 1x1nA 524 4.57e+01 c.1.8.1 121593 2qrwA 128 4.57e+01 3kczA 368 4.57e+01 1z8uA 102 4.59e+01 a.7.11.1 124724 1gqeA 365 4.62e+01 e.38.1.1 70351 1u4qA 322 4.71e+01 a.7.1.1,a.7.1.1,a.7.1.1 113024,113025,113026 2e7sA 135 4.74e+01 h.1.33.1 132068 2nppB 449 4.77e+01 a.118.1.20 138445 3dbaA 180 4.78e+01 1ngkA 128 4.80e+01 a.1.1.1 85673 3hr0A 263 4.81e+01 3cx5F 146 4.87e+01 f.28.1.1 157086 2zq8A 262 4.93e+01 3hhyA 280 4.95e+01 1k28A 584 4.96e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1ybkA 52 4.97e+01 2zdiC 151 4.98e+01 2vccA 891 5.02e+01 1epwA 1290 5.06e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1r2fA 319 5.11e+01 1r2fA a.25.1.2 16800 2zq7A 262 5.15e+01 1zoqC 47 5.15e+01 a.153.1.1 125453 1ecmA 109 5.18e+01 1ecmA a.130.1.1 19492 3a03A 56 5.23e+01 2p6vA 114 5.28e+01 a.277.1.1 149278 3m5wA 322 5.30e+01 1vqtA 213 5.34e+01 c.1.2.3 120417 2jekA 145 5.41e+01 a.255.1.1 138286 1u6hB 31 5.44e+01 3fn2A 106 5.44e+01 1ls9A 91 5.45e+01 a.3.1.1 78177 2incB 322 5.46e+01 a.25.1.2 137525 1ykhB 132 5.56e+01 a.252.1.1 123519 1xl3C 92 5.58e+01 a.243.1.1 122104 2atsA 292 5.61e+01 c.1.10.1 127306 2g7lA 243 5.61e+01 a.4.1.9,a.121.1.1 134734,134735 2qpqA 301 5.61e+01 1nc5A 373 5.63e+01 a.102.1.6 85548 2a6nA 292 5.65e+01 c.1.10.1 126289 1d3yA 301 5.70e+01 1d3yA e.12.1.1 43252 3h0lC 94 5.71e+01 1fxkB 109 5.82e+01 1fxkA a.2.5.1 15704 3glrA 285 5.86e+01 3f7sA 142 5.87e+01 2gf4A 100 5.87e+01 a.8.10.1 135074 2j7qA 232 5.88e+01 d.3.1.20 145673 3fydA 263 5.90e+01 2purA 292 5.90e+01 1t5oA 351 5.90e+01 c.124.1.5 106459 2f2gA 221 5.90e+01 a.132.1.3 132816 1qqfA 277 5.92e+01 1c3d a.102.4.4 18875 1sf9A 128 5.92e+01 b.34.15.1 98831 3d9hA 285 5.94e+01 1cqmA 101 5.95e+01 1ris d.58.14.1 39321 3kwqB 83 5.99e+01 2nxpA 156 6.05e+01 d.379.1.1 148504 2anxA 146 6.06e+01 1d8hA 311 6.07e+01 1d8iA d.63.1.1 39544 2po3A 424 6.11e+01 2bcqA 335 6.16e+01 a.60.6.1,a.60.12.1,d.218.1.2 128304,128305,128306 2je6A 277 6.17e+01 d.14.1.4,d.101.1.1 147991,147992 1m5iA 125 6.18e+01 h.4.13.1 78648 1h97A 147 6.23e+01 1h97A a.1.1.2 60812 2wi8A 311 6.34e+01 3gruA 295 6.34e+01 3d1cA 369 6.43e+01 2r91A 286 6.43e+01 1orsC 132 6.48e+01 f.14.1.1 87353 2ej5A 257 6.48e+01 2vzbA 170 6.54e+01 1j7lA 264 6.58e+01 d.144.1.6 62697 3ibxA 221 6.61e+01 2wieA 82 6.64e+01 1n1jB 97 6.65e+01 a.22.1.3 79814 2rh1A 500 6.68e+01 2f37A 251 6.70e+01 3lypA 215 6.72e+01 1j1dB 106 6.76e+01 h.1.25.1 83964 2ogfA 122 6.80e+01 1mw9X 592 6.83e+01 e.10.1.1 91480 1zvzA 279 6.84e+01 2o02A 230 6.88e+01 a.118.7.1 148541 1t3wA 148 6.92e+01 a.236.1.1 112233 1f5aA 513 6.93e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 3hq1A 644 6.95e+01 3e7pA 270 6.98e+01 3hhcA 196 7.00e+01 3c9pA 123 7.06e+01 3mdkA 217 7.09e+01 1zpyA 95 7.13e+01 a.25.1.5 125479 3m9vA 439 7.22e+01 1rt8A 513 7.23e+01 a.40.1.1 105095 3ivyA 433 7.24e+01 1bjt 793 7.24e+01 1bjt 1bjtA 793 7.24e+01 e.11.1.1 43249 137lA 164 7.26e+01 1l92 d.2.1.3 36791 1p36A 164 7.26e+01 d.2.1.3 93978 3g89A 249 7.27e+01 2gtsA 86 7.30e+01 a.25.5.1 147176 1rp3A 239 7.30e+01 a.4.13.1,a.4.13.2,a.177.1.1 97678,97679,97680 1q77A 138 7.35e+01 c.26.2.4 96023 1j5wA 298 7.36e+01 d.104.1.1 71589 1z1bA 356 7.36e+01 d.10.1.4,d.163.1.1 124346,124347 2fbhA 146 7.37e+01 a.4.5.28 133245 1kfrA 147 7.38e+01 a.1.1.2 72424 3gfmA 146 7.44e+01 1rztA 331 7.45e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1ydiA 263 7.49e+01 2z6vA 414 7.50e+01 3l1nA 194 7.51e+01 1y8oA 419 7.53e+01 a.29.5.1,d.122.1.4 144603,144604 1t0qB 330 7.56e+01 a.25.1.2 106221 1aoa 275 7.59e+01 1aoa 1s9aA 257 7.61e+01 b.3.6.1 105379 1u5pA 216 7.66e+01 a.7.1.1,a.7.1.1 113046,113047 2qzcA 214 7.71e+01 1vliA 385 7.76e+01 b.85.1.1,c.1.10.6 108830,108831 2hd1A 326 7.82e+01 a.211.1.2 136338 3dr0A 93 7.85e+01 2oifA 162 7.85e+01 1i7dA 659 7.87e+01 1d6mA e.10.1.1 61886 1tbfA 347 7.90e+01 a.211.1.2 106743 3iukA 562 7.93e+01 2p54A 267 7.94e+01 a.123.1.1 139497 3c2eA 294 7.99e+01